The main effect of the Reformation was the breaking of the monolithic power of the Roman Catholic Church. This led to a greater freedom of inquiry in many areas, as intellectual life was not dominated by Thomism in Protestant countries.
One major effect of the sola scriptura doctrine of Protestantism was a rise in vernacular literacy, due to the new emphasis on the laity reading the Bible for themselves, and an ensuing rise in vernacular literature.
Scientific inquiry flourished as it was no longer constrained by Aristotelian doctrines being treated as infallible dogma.
Because Protestantism emphasized the historical Jesus rather than the church magisterium, it led to the development of scientific philology, and ultimately higher and lower criticism.